Query 045954
Match_columns 76
No_of_seqs 110 out of 342
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 07:16:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045954.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045954hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00158 histone H2B; Provisio 100.0 9E-31 2E-35 178.7 5.1 73 1-76 1-104 (116)
2 PTZ00463 histone H2B; Provisio 100.0 3.6E-30 7.9E-35 176.0 6.3 56 21-76 19-105 (117)
3 smart00427 H2B Histone H2B. 99.9 6.1E-27 1.3E-31 153.7 4.6 47 30-76 1-78 (89)
4 KOG1744 Histone H2B [Chromatin 99.9 1.4E-24 3.1E-29 150.1 3.9 58 19-76 26-114 (127)
5 PF00125 Histone: Core histone 98.3 7.8E-07 1.7E-11 53.7 3.1 37 28-64 3-74 (75)
6 smart00803 TAF TATA box bindin 91.4 0.34 7.4E-06 29.6 3.5 30 34-63 34-65 (65)
7 cd00074 H2A Histone 2A; H2A is 89.2 0.72 1.6E-05 31.3 3.9 35 30-64 41-85 (115)
8 cd07979 TAF9 TATA Binding Prot 88.2 1 2.2E-05 30.3 4.1 33 35-67 34-68 (117)
9 PLN00035 histone H4; Provision 88.2 1.2 2.5E-05 30.1 4.3 21 44-64 73-93 (103)
10 cd00076 H4 Histone H4, one of 87.5 1.4 3.1E-05 28.5 4.3 32 33-64 44-77 (85)
11 PTZ00015 histone H4; Provision 87.2 1.4 3.1E-05 29.5 4.3 21 44-64 74-94 (102)
12 cd07981 TAF12 TATA Binding Pro 87.1 1.6 3.4E-05 26.8 4.2 32 33-64 33-66 (72)
13 PF02969 TAF: TATA box binding 86.5 0.96 2.1E-05 28.1 3.0 20 44-63 47-66 (66)
14 COG2036 HHT1 Histones H3 and H 86.3 1.8 3.8E-05 28.5 4.3 25 44-68 63-87 (91)
15 PF00808 CBFD_NFYB_HMF: Histon 83.3 2.6 5.7E-05 24.7 3.8 30 33-62 34-65 (65)
16 smart00428 H3 Histone H3. 79.2 4.4 9.5E-05 27.2 4.1 32 34-65 68-101 (105)
17 PF04157 EAP30: EAP30/Vps36 fa 75.9 4.1 8.9E-05 29.3 3.5 37 30-66 86-146 (223)
18 PLN00154 histone H2A; Provisio 71.4 5.5 0.00012 28.2 3.1 33 31-63 61-103 (136)
19 smart00417 H4 Histone H4. 70.8 6.9 0.00015 24.8 3.2 16 44-59 57-72 (74)
20 cd08050 TAF6 TATA Binding Prot 65.6 11 0.00025 29.0 4.1 22 44-65 43-64 (343)
21 PTZ00017 histone H2A; Provisio 64.5 8.7 0.00019 27.0 3.0 33 31-63 49-91 (134)
22 PF02291 TFIID-31kDa: Transcri 64.0 15 0.00034 25.3 4.1 33 34-66 44-78 (129)
23 smart00414 H2A Histone 2A. 63.6 11 0.00024 25.1 3.3 34 30-63 30-73 (106)
24 PF03847 TFIID_20kDa: Transcri 62.9 10 0.00022 23.4 2.8 31 33-63 31-63 (68)
25 PLN00121 histone H3; Provision 60.7 13 0.00027 26.2 3.3 21 44-64 111-131 (136)
26 PF12763 EF-hand_4: Cytoskelet 59.9 11 0.00024 24.7 2.8 28 38-65 43-72 (104)
27 KOG3334 Transcription initiati 59.6 19 0.00041 26.0 4.0 32 34-65 45-78 (148)
28 PF02885 Glycos_trans_3N: Glyc 56.6 12 0.00026 22.1 2.3 31 41-71 3-33 (66)
29 PTZ00018 histone H3; Provision 56.2 17 0.00036 25.6 3.2 21 44-64 111-131 (136)
30 PF05258 DUF721: Protein of un 54.0 16 0.00036 21.4 2.6 24 51-74 18-41 (89)
31 PLN00160 histone H3; Provision 53.1 24 0.00052 23.5 3.5 32 33-64 58-91 (97)
32 PLN00161 histone H3; Provision 51.9 27 0.00059 24.6 3.8 21 44-64 105-125 (135)
33 PLN00157 histone H2A; Provisio 51.8 19 0.00042 25.2 3.0 34 30-63 47-90 (132)
34 PLN00153 histone H2A; Provisio 51.7 23 0.0005 24.8 3.3 34 30-63 45-88 (129)
35 PF14374 Ribos_L4_asso_C: 60S 50.8 2.7 5.8E-05 27.1 -1.3 12 52-63 18-29 (80)
36 PF00607 Gag_p24: gag gene pro 50.8 25 0.00055 25.4 3.6 20 24-43 128-147 (206)
37 PF14513 DAG_kinase_N: Diacylg 49.9 20 0.00043 25.0 2.8 44 30-73 17-73 (138)
38 PLN00156 histone H2AX; Provisi 48.8 28 0.00061 24.7 3.4 33 31-63 51-93 (139)
39 smart00576 BTP Bromodomain tra 46.6 66 0.0014 19.5 4.6 33 32-64 36-70 (77)
40 PF15630 CENP-S: Kinetochore c 46.4 25 0.00055 22.1 2.7 31 33-63 35-71 (76)
41 TIGR02442 Cob-chelat-sub cobal 44.8 38 0.00082 28.2 4.1 27 44-70 283-309 (633)
42 PF03477 ATP-cone: ATP cone do 42.4 33 0.00071 20.7 2.7 33 34-66 35-69 (90)
43 TIGR02031 BchD-ChlD magnesium 37.5 59 0.0013 26.9 4.2 27 44-70 237-263 (589)
44 CHL00081 chlI Mg-protoporyphyr 35.9 65 0.0014 25.3 4.0 27 44-70 301-327 (350)
45 KOG3090 Prohibitin-like protei 35.4 25 0.00053 27.6 1.6 36 34-72 132-167 (290)
46 COG2361 Uncharacterized conser 33.4 1E+02 0.0022 21.3 4.2 45 29-73 3-55 (117)
47 PTZ00252 histone H2A; Provisio 33.0 63 0.0014 22.8 3.2 34 30-63 46-91 (134)
48 TIGR02030 BchI-ChlI magnesium 32.5 44 0.00094 25.9 2.6 27 44-70 288-314 (337)
49 TIGR00630 uvra excinuclease AB 30.9 20 0.00044 31.7 0.5 43 25-67 48-111 (924)
50 KOG1756 Histone 2A [Chromatin 30.0 99 0.0021 21.9 3.8 20 44-63 72-91 (131)
51 PF09193 CholecysA-Rec_N: Chol 28.9 19 0.00042 21.4 0.1 13 54-66 35-47 (47)
52 PRK00349 uvrA excinuclease ABC 28.9 23 0.00049 31.4 0.5 43 25-67 52-115 (943)
53 KOG3083 Prohibitin [Posttransl 28.8 54 0.0012 25.6 2.5 25 37-61 124-148 (271)
54 PF14164 YqzH: YqzH-like prote 26.8 1.6E+02 0.0035 18.4 4.0 31 34-64 4-37 (64)
55 COG5262 HTA1 Histone H2A [Chro 25.9 1E+02 0.0022 21.8 3.2 31 33-63 50-90 (132)
56 PRK13406 bchD magnesium chelat 25.7 1.1E+02 0.0025 25.6 4.0 27 44-70 229-255 (584)
57 KOG2549 Transcription initiati 25.5 76 0.0016 27.3 3.0 22 44-65 55-76 (576)
58 KOG1142 Transcription initiati 25.3 47 0.001 25.8 1.6 26 44-69 199-228 (258)
59 PF12412 DUF3667: Protein of u 23.9 61 0.0013 18.4 1.6 16 58-73 5-21 (46)
60 KOG1745 Histones H3 and H4 [Ch 23.9 21 0.00046 25.3 -0.4 22 44-65 112-133 (137)
61 PF11460 DUF3007: Protein of u 23.2 31 0.00068 23.4 0.3 40 33-72 51-97 (104)
62 KOG0869 CCAAT-binding factor, 23.1 99 0.0021 22.7 2.9 22 44-65 78-99 (168)
63 PF04406 TP6A_N: Type IIB DNA 22.8 88 0.0019 18.5 2.2 25 34-58 9-33 (68)
64 KOG0870 DNA polymerase epsilon 21.9 2E+02 0.0042 21.3 4.2 33 32-65 46-78 (172)
65 PHA02937 hypothetical protein; 21.9 74 0.0016 25.2 2.1 15 29-43 16-30 (310)
66 PRK00464 nrdR transcriptional 20.5 1.4E+02 0.0031 21.0 3.2 16 51-66 101-116 (154)
No 1
>PLN00158 histone H2B; Provisional
Probab=99.96 E-value=9e-31 Score=178.74 Aligned_cols=73 Identities=59% Similarity=0.846 Sum_probs=59.6
Q ss_pred CCCCCcccccccccccCCcccccccccCcchhHHHHHHHHHHH-------------------------------HHhhcC
Q 045954 1 MANKPKVGKKLSKKATSSNKEKKCAKKSIKTYNIYIFKVLKQV-------------------------------FARYKK 49 (76)
Q Consensus 1 ~~~~~~~~~~~~~~~~~g~~~kkrkkkr~esy~~YiykVLKqV-------------------------------La~~nk 49 (76)
|+|.|. +++..+... ..+++++++|+|+|++||||||||| |++||+
T Consensus 1 ~~~~~~--~k~~~~~~~-~~~kk~~~kr~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nk 77 (116)
T PLN00158 1 MAKTPS--KKPAKKAAK-GAKKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNK 77 (116)
T ss_pred CCCCcc--hhhhhhccc-cccccccccccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 566643 333222222 2356677788999999999999999 999999
Q ss_pred CCCcchHHHHHHHHhhcchhhhhhccC
Q 045954 50 KPMITSWEFHTVGRLVLPGELAKHTVF 76 (76)
Q Consensus 50 r~TitsrEIqtAvrLlLPGELaKhAvs 76 (76)
++|||+|||||||||||||||+|||||
T Consensus 78 r~TltsrEIqtAvrLvLpgELaKhAvs 104 (116)
T PLN00158 78 KPTVTSREIQTAVRLILPGELAKHAVS 104 (116)
T ss_pred CCcCCHHHHHHHHHHhccHHHHHHHHH
Confidence 999999999999999999999999985
No 2
>PTZ00463 histone H2B; Provisional
Probab=99.96 E-value=3.6e-30 Score=176.04 Aligned_cols=56 Identities=52% Similarity=0.808 Sum_probs=52.6
Q ss_pred cccccccCcchhHHHHHHHHHHH-------------------------------HHhhcCCCCcchHHHHHHHHhhcchh
Q 045954 21 EKKCAKKSIKTYNIYIFKVLKQV-------------------------------FARYKKKPMITSWEFHTVGRLVLPGE 69 (76)
Q Consensus 21 ~kkrkkkr~esy~~YiykVLKqV-------------------------------La~~nkr~TitsrEIqtAvrLlLPGE 69 (76)
+++++++|.|||++||||||||| |++||+++|||+|||||||||+||||
T Consensus 19 ~kk~~~kr~esy~~YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLlLpGE 98 (117)
T PTZ00463 19 KKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGE 98 (117)
T ss_pred cccccccccchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhcccHH
Confidence 35667778999999999999999 99999999999999999999999999
Q ss_pred hhhhccC
Q 045954 70 LAKHTVF 76 (76)
Q Consensus 70 LaKhAvs 76 (76)
|+|||||
T Consensus 99 LaKhAvs 105 (117)
T PTZ00463 99 LAKHAVS 105 (117)
T ss_pred HHHhhhh
Confidence 9999986
No 3
>smart00427 H2B Histone H2B.
Probab=99.93 E-value=6.1e-27 Score=153.67 Aligned_cols=47 Identities=64% Similarity=0.966 Sum_probs=45.9
Q ss_pred chhHHHHHHHHHHH-------------------------------HHhhcCCCCcchHHHHHHHHhhcchhhhhhccC
Q 045954 30 KTYNIYIFKVLKQV-------------------------------FARYKKKPMITSWEFHTVGRLVLPGELAKHTVF 76 (76)
Q Consensus 30 esy~~YiykVLKqV-------------------------------La~~nkr~TitsrEIqtAvrLlLPGELaKhAvs 76 (76)
|||++||||||||| |++||+++|||+|||||||||+|||||+||||+
T Consensus 1 esy~~Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~LpgeLakhAvs 78 (89)
T smart00427 1 ETYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVS 78 (89)
T ss_pred CcHHHHHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHHccHHHHHHHHH
Confidence 79999999999999 999999999999999999999999999999986
No 4
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=99.90 E-value=1.4e-24 Score=150.14 Aligned_cols=58 Identities=48% Similarity=0.745 Sum_probs=54.3
Q ss_pred cccccccccCcchhHHHHHHHHHHH-------------------------------HHhhcCCCCcchHHHHHHHHhhcc
Q 045954 19 NKEKKCAKKSIKTYNIYIFKVLKQV-------------------------------FARYKKKPMITSWEFHTVGRLVLP 67 (76)
Q Consensus 19 ~~~kkrkkkr~esy~~YiykVLKqV-------------------------------La~~nkr~TitsrEIqtAvrLlLP 67 (76)
+.+|++..++.|+|+.||||||||| |++||+|+|||||||||||||+||
T Consensus 26 k~gk~~~~~~~e~~s~yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLllP 105 (127)
T KOG1744|consen 26 KAGKKRSTRRKESYSEYVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLLLP 105 (127)
T ss_pred cccccCcccccCceeeehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHhCc
Confidence 3357778899999999999999999 999999999999999999999999
Q ss_pred hhhhhhccC
Q 045954 68 GELAKHTVF 76 (76)
Q Consensus 68 GELaKhAvs 76 (76)
|||+|||+|
T Consensus 106 gel~khA~s 114 (127)
T KOG1744|consen 106 GELAKHAVS 114 (127)
T ss_pred hHHhhhhhc
Confidence 999999986
No 5
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=98.28 E-value=7.8e-07 Score=53.73 Aligned_cols=37 Identities=19% Similarity=0.262 Sum_probs=32.0
Q ss_pred CcchhHHHHHHHHHHH-----------------------------------HHhhcCCCCcchHHHHHHHHh
Q 045954 28 SIKTYNIYIFKVLKQV-----------------------------------FARYKKKPMITSWEFHTVGRL 64 (76)
Q Consensus 28 r~esy~~YiykVLKqV-----------------------------------La~~nkr~TitsrEIqtAvrL 64 (76)
+...+..||.||+++| ++.+++|.||+++|||.|+++
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~ 74 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRI 74 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhc
Confidence 4566778888888877 889999999999999999986
No 6
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=91.45 E-value=0.34 Score=29.60 Aligned_cols=30 Identities=20% Similarity=0.350 Sum_probs=22.6
Q ss_pred HHHHHHHHHH--HHhhcCCCCcchHHHHHHHH
Q 045954 34 IYIFKVLKQV--FARYKKKPMITSWEFHTVGR 63 (76)
Q Consensus 34 ~YiykVLKqV--La~~nkr~TitsrEIqtAvr 63 (76)
.|+..|+++. ++++.+|.|+|..||.-|++
T Consensus 34 ~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 34 YRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred HHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 3444444444 99999999999999988764
No 7
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=89.22 E-value=0.72 Score=31.31 Aligned_cols=35 Identities=29% Similarity=0.269 Sum_probs=29.6
Q ss_pred chhHHHHHHHHHHH----------HHhhcCCCCcchHHHHHHHHh
Q 045954 30 KTYNIYIFKVLKQV----------FARYKKKPMITSWEFHTVGRL 64 (76)
Q Consensus 30 esy~~YiykVLKqV----------La~~nkr~TitsrEIqtAvrL 64 (76)
++-.+|+--||.-+ .++.+++.+||+++|+.|++-
T Consensus 41 ~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 41 AGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 44578888888776 788999999999999999973
No 8
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=88.18 E-value=1 Score=30.26 Aligned_cols=33 Identities=15% Similarity=0.151 Sum_probs=26.3
Q ss_pred HHHHHHHHH--HHhhcCCCCcchHHHHHHHHhhcc
Q 045954 35 YIFKVLKQV--FARYKKKPMITSWEFHTVGRLVLP 67 (76)
Q Consensus 35 YiykVLKqV--La~~nkr~TitsrEIqtAvrLlLP 67 (76)
|+..||++. ++.+.+|.||+..||.-|+...+.
T Consensus 34 y~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 34 YTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence 444444444 999999999999999999988765
No 9
>PLN00035 histone H4; Provisional
Probab=88.16 E-value=1.2 Score=30.08 Aligned_cols=21 Identities=5% Similarity=0.137 Sum_probs=19.3
Q ss_pred HHhhcCCCCcchHHHHHHHHh
Q 045954 44 FARYKKKPMITSWEFHTVGRL 64 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvrL 64 (76)
++.+.+|.||+..||--|++.
T Consensus 73 ya~HA~RKTV~~~DV~~Alkr 93 (103)
T PLN00035 73 YTEHARRKTVTAMDVVYALKR 93 (103)
T ss_pred HHHhcCCCcCcHHHHHHHHHH
Confidence 889999999999999988874
No 10
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=87.52 E-value=1.4 Score=28.52 Aligned_cols=32 Identities=13% Similarity=0.263 Sum_probs=23.6
Q ss_pred HHHHHHHHHHH--HHhhcCCCCcchHHHHHHHHh
Q 045954 33 NIYIFKVLKQV--FARYKKKPMITSWEFHTVGRL 64 (76)
Q Consensus 33 ~~YiykVLKqV--La~~nkr~TitsrEIqtAvrL 64 (76)
..|+-.|+++. ++.+.+|.|||..||--|++.
T Consensus 44 ~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr 77 (85)
T cd00076 44 KSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKR 77 (85)
T ss_pred HHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence 33444444443 889999999999999888763
No 11
>PTZ00015 histone H4; Provisional
Probab=87.23 E-value=1.4 Score=29.54 Aligned_cols=21 Identities=10% Similarity=0.295 Sum_probs=19.0
Q ss_pred HHhhcCCCCcchHHHHHHHHh
Q 045954 44 FARYKKKPMITSWEFHTVGRL 64 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvrL 64 (76)
++.|.+|.|||..||--|++.
T Consensus 74 ~aeHA~RKTVt~~DV~~AlKr 94 (102)
T PTZ00015 74 YTEYARRKTVTAMDVVYALKR 94 (102)
T ss_pred HHHhcCCCcccHHHHHHHHHh
Confidence 899999999999999888764
No 12
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=87.13 E-value=1.6 Score=26.78 Aligned_cols=32 Identities=9% Similarity=0.130 Sum_probs=24.9
Q ss_pred HHHHHHHHHHH--HHhhcCCCCcchHHHHHHHHh
Q 045954 33 NIYIFKVLKQV--FARYKKKPMITSWEFHTVGRL 64 (76)
Q Consensus 33 ~~YiykVLKqV--La~~nkr~TitsrEIqtAvrL 64 (76)
..|+-.|++.. ||.+.++.||..+|||-++.-
T Consensus 33 e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r 66 (72)
T cd07981 33 DDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER 66 (72)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 34555555555 999999999999999988763
No 13
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=86.49 E-value=0.96 Score=28.07 Aligned_cols=20 Identities=25% Similarity=0.366 Sum_probs=16.1
Q ss_pred HHhhcCCCCcchHHHHHHHH
Q 045954 44 FARYKKKPMITSWEFHTVGR 63 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvr 63 (76)
++++.+|.+||..||..|.|
T Consensus 47 fm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 47 FMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp HHHHTT-SSB-HHHHHHHH-
T ss_pred HHHHhCCCCCCHHHHHHHhC
Confidence 89999999999999999875
No 14
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=86.31 E-value=1.8 Score=28.51 Aligned_cols=25 Identities=8% Similarity=0.024 Sum_probs=22.7
Q ss_pred HHhhcCCCCcchHHHHHHHHhhcch
Q 045954 44 FARYKKKPMITSWEFHTVGRLVLPG 68 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvrLlLPG 68 (76)
+|.+.+|.||+..||+-|++.+-+.
T Consensus 63 ~A~ha~RKTV~~~DI~la~~~~~~~ 87 (91)
T COG2036 63 LAEHAKRKTVKAEDIKLALKRLGRR 87 (91)
T ss_pred HHHHcCCCeecHHHHHHHHHHhccc
Confidence 8999999999999999999987654
No 15
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=83.27 E-value=2.6 Score=24.69 Aligned_cols=30 Identities=20% Similarity=0.176 Sum_probs=21.9
Q ss_pred HHHHHHHHHHH--HHhhcCCCCcchHHHHHHH
Q 045954 33 NIYIFKVLKQV--FARYKKKPMITSWEFHTVG 62 (76)
Q Consensus 33 ~~YiykVLKqV--La~~nkr~TitsrEIqtAv 62 (76)
..||.-+..+. .+..++|.||+.+||.+||
T Consensus 34 e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 34 EEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 34555555554 7788999999999999986
No 16
>smart00428 H3 Histone H3.
Probab=79.21 E-value=4.4 Score=27.23 Aligned_cols=32 Identities=16% Similarity=0.273 Sum_probs=25.5
Q ss_pred HHHHHHHHHH--HHhhcCCCCcchHHHHHHHHhh
Q 045954 34 IYIFKVLKQV--FARYKKKPMITSWEFHTVGRLV 65 (76)
Q Consensus 34 ~YiykVLKqV--La~~nkr~TitsrEIqtAvrLl 65 (76)
.|+-.+++.. ++.+.+|-||..+|||-|.++-
T Consensus 68 ~ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir 101 (105)
T smart00428 68 AYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIR 101 (105)
T ss_pred HHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHh
Confidence 3555555554 8899999999999999998853
No 17
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=75.94 E-value=4.1 Score=29.28 Aligned_cols=37 Identities=16% Similarity=0.382 Sum_probs=30.7
Q ss_pred chhHHHHHHHHHHH--------------------HHhhcCCC----CcchHHHHHHHHhhc
Q 045954 30 KTYNIYIFKVLKQV--------------------FARYKKKP----MITSWEFHTVGRLVL 66 (76)
Q Consensus 30 esy~~YiykVLKqV--------------------La~~nkr~----TitsrEIqtAvrLlL 66 (76)
.+.+.|.|.+-.|| ++.||+.. .||+.||..|+.++=
T Consensus 86 ~~~~~f~~ELa~qi~e~c~~~~~~~GGii~L~dl~~~~nr~R~g~~lISp~Di~~A~~~l~ 146 (223)
T PF04157_consen 86 KGSGDFYYELAVQIAEVCLATRSKNGGIISLSDLYCRYNRARGGSELISPEDILRACKLLE 146 (223)
T ss_dssp SCHHHHHHHHHHHHHHHHHHHCCTTTSEEEHHHHHHHHHHCTTTSST--HHHHHHHHHHHC
T ss_pred ccchhHHHHHHHHHHHHHHHHHhcCCCEEEHHHHHHHHHHhcccCCCcCHHHHHHHHHHHH
Confidence 47789999999999 78888887 899999999999873
No 18
>PLN00154 histone H2A; Provisional
Probab=71.38 E-value=5.5 Score=28.18 Aligned_cols=33 Identities=21% Similarity=0.201 Sum_probs=27.8
Q ss_pred hhHHHHHHHHHHH----------HHhhcCCCCcchHHHHHHHH
Q 045954 31 TYNIYIFKVLKQV----------FARYKKKPMITSWEFHTVGR 63 (76)
Q Consensus 31 sy~~YiykVLKqV----------La~~nkr~TitsrEIqtAvr 63 (76)
+-.+|+--||.=+ -++.+++.-||+|.||.|++
T Consensus 61 ~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 61 TAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 3568888888766 56789999999999999997
No 19
>smart00417 H4 Histone H4.
Probab=70.84 E-value=6.9 Score=24.80 Aligned_cols=16 Identities=6% Similarity=0.297 Sum_probs=14.6
Q ss_pred HHhhcCCCCcchHHHH
Q 045954 44 FARYKKKPMITSWEFH 59 (76)
Q Consensus 44 La~~nkr~TitsrEIq 59 (76)
++.+.+|.|+++.||-
T Consensus 57 ~a~ha~RKTV~~~DV~ 72 (74)
T smart00417 57 YTEHARRKTVTAMDVV 72 (74)
T ss_pred HHHhcCCCcccHHHhe
Confidence 8999999999999974
No 20
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=65.62 E-value=11 Score=29.01 Aligned_cols=22 Identities=27% Similarity=0.336 Sum_probs=20.7
Q ss_pred HHhhcCCCCcchHHHHHHHHhh
Q 045954 44 FARYKKKPMITSWEFHTVGRLV 65 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvrLl 65 (76)
+++..+|.||+..||..|++..
T Consensus 43 ~~~hskR~~l~~~Di~~Al~~~ 64 (343)
T cd08050 43 FMRHSKRRKLTTSDVNHALRLR 64 (343)
T ss_pred HHHHhCCCcCCHHHHHHHHHHh
Confidence 9999999999999999999864
No 21
>PTZ00017 histone H2A; Provisional
Probab=64.48 E-value=8.7 Score=26.99 Aligned_cols=33 Identities=27% Similarity=0.277 Sum_probs=27.6
Q ss_pred hhHHHHHHHHHHH----------HHhhcCCCCcchHHHHHHHH
Q 045954 31 TYNIYIFKVLKQV----------FARYKKKPMITSWEFHTVGR 63 (76)
Q Consensus 31 sy~~YiykVLKqV----------La~~nkr~TitsrEIqtAvr 63 (76)
+-.+|+--||.-+ -++.+++.-||+|.||.|++
T Consensus 49 ~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 49 GAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred cchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 4567888887766 56789999999999999997
No 22
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=64.02 E-value=15 Score=25.26 Aligned_cols=33 Identities=18% Similarity=0.175 Sum_probs=23.1
Q ss_pred HHHHHHHHHH--HHhhcCCCCcchHHHHHHHHhhc
Q 045954 34 IYIFKVLKQV--FARYKKKPMITSWEFHTVGRLVL 66 (76)
Q Consensus 34 ~YiykVLKqV--La~~nkr~TitsrEIqtAvrLlL 66 (76)
.|+..||.+- .+.+.++.+|+..||+-|+..-+
T Consensus 44 RYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~ 78 (129)
T PF02291_consen 44 RYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRL 78 (129)
T ss_dssp HHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-
T ss_pred HHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHH
Confidence 3555555544 88899999999999999998553
No 23
>smart00414 H2A Histone 2A.
Probab=63.57 E-value=11 Score=25.14 Aligned_cols=34 Identities=29% Similarity=0.292 Sum_probs=28.1
Q ss_pred chhHHHHHHHHHHH----------HHhhcCCCCcchHHHHHHHH
Q 045954 30 KTYNIYIFKVLKQV----------FARYKKKPMITSWEFHTVGR 63 (76)
Q Consensus 30 esy~~YiykVLKqV----------La~~nkr~TitsrEIqtAvr 63 (76)
.+-.+|+--||.-+ -++.+++.-||++.||.|++
T Consensus 30 ~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~ 73 (106)
T smart00414 30 AGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIR 73 (106)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhcc
Confidence 44578988888766 46778899999999999987
No 24
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=62.89 E-value=10 Score=23.37 Aligned_cols=31 Identities=10% Similarity=0.120 Sum_probs=22.7
Q ss_pred HHHHHHHHHHH--HHhhcCCCCcchHHHHHHHH
Q 045954 33 NIYIFKVLKQV--FARYKKKPMITSWEFHTVGR 63 (76)
Q Consensus 33 ~~YiykVLKqV--La~~nkr~TitsrEIqtAvr 63 (76)
..||..|+.+. ||++.+..||..+|||-...
T Consensus 31 ddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Le 63 (68)
T PF03847_consen 31 DDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLE 63 (68)
T ss_dssp HHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHH
Confidence 45666666666 99999999999999996543
No 25
>PLN00121 histone H3; Provisional
Probab=60.68 E-value=13 Score=26.20 Aligned_cols=21 Identities=19% Similarity=0.170 Sum_probs=19.0
Q ss_pred HHhhcCCCCcchHHHHHHHHh
Q 045954 44 FARYKKKPMITSWEFHTVGRL 64 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvrL 64 (76)
.+.+.+|-||..+|||-+.||
T Consensus 111 ca~HakRVTl~~kD~~L~~ri 131 (136)
T PLN00121 111 CAIHAKRVTIMPKDIQLARRI 131 (136)
T ss_pred HHHHhcceecchhhHHHHHHh
Confidence 778999999999999999874
No 26
>PF12763 EF-hand_4: Cytoskeletal-regulatory complex EF hand; PDB: 2QPT_A 2KSP_A 2KFG_A 2JQ6_A 2KFH_A 2KFF_A 1IQ3_A 3FIA_A 2KHN_A 2KGR_A ....
Probab=59.93 E-value=11 Score=24.70 Aligned_cols=28 Identities=25% Similarity=0.296 Sum_probs=25.1
Q ss_pred HHHHHH--HHhhcCCCCcchHHHHHHHHhh
Q 045954 38 KVLKQV--FARYKKKPMITSWEFHTVGRLV 65 (76)
Q Consensus 38 kVLKqV--La~~nkr~TitsrEIqtAvrLl 65 (76)
.+|.|| |+..++.-.|+-.|+-.|++|+
T Consensus 43 ~~L~~IW~LaD~~~dG~L~~~EF~iAm~Li 72 (104)
T PF12763_consen 43 DVLAQIWNLADIDNDGKLDFEEFAIAMHLI 72 (104)
T ss_dssp HHHHHHHHHH-SSSSSEEEHHHHHHHHHHH
T ss_pred HHHHHHHhhhcCCCCCcCCHHHHHHHHHHH
Confidence 678888 9999999999999999999987
No 27
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=59.60 E-value=19 Score=25.96 Aligned_cols=32 Identities=22% Similarity=0.264 Sum_probs=24.9
Q ss_pred HHHHHHHHH--HHHhhcCCCCcchHHHHHHHHhh
Q 045954 34 IYIFKVLKQ--VFARYKKKPMITSWEFHTVGRLV 65 (76)
Q Consensus 34 ~YiykVLKq--VLa~~nkr~TitsrEIqtAvrLl 65 (76)
.|+-.||.. |.+.+.++.||+..||+.|+...
T Consensus 45 rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~ 78 (148)
T KOG3334|consen 45 RYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMR 78 (148)
T ss_pred HHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHH
Confidence 344455542 28899999999999999999865
No 28
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=56.63 E-value=12 Score=22.09 Aligned_cols=31 Identities=16% Similarity=0.282 Sum_probs=19.0
Q ss_pred HHHHHhhcCCCCcchHHHHHHHHhhcchhhh
Q 045954 41 KQVFARYKKKPMITSWEFHTVGRLVLPGELA 71 (76)
Q Consensus 41 KqVLa~~nkr~TitsrEIqtAvrLlLPGELa 71 (76)
+++|.+......+|..|+..+++.++-|++.
T Consensus 3 ~~~l~~l~~g~~Ls~~e~~~~~~~i~~g~~s 33 (66)
T PF02885_consen 3 KEILKKLRDGEDLSREEAKAAFDAILDGEVS 33 (66)
T ss_dssp HHHHHHHHTT----HHHHHHHHHHHHTTSS-
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHHHHcCCCC
Confidence 3344444445899999999999999988764
No 29
>PTZ00018 histone H3; Provisional
Probab=56.18 E-value=17 Score=25.63 Aligned_cols=21 Identities=19% Similarity=0.170 Sum_probs=18.8
Q ss_pred HHhhcCCCCcchHHHHHHHHh
Q 045954 44 FARYKKKPMITSWEFHTVGRL 64 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvrL 64 (76)
.+.+.+|-||..+|||-|.||
T Consensus 111 ca~HakRVTl~~kD~~L~~ri 131 (136)
T PTZ00018 111 CAIHAKRVTIMPKDIQLARRI 131 (136)
T ss_pred HHHhhcceecchhhHHHHHHh
Confidence 677899999999999999874
No 30
>PF05258 DUF721: Protein of unknown function (DUF721); InterPro: IPR007922 This family contains several actinomycete proteins of unknown function, and related sequences from other species.
Probab=53.97 E-value=16 Score=21.38 Aligned_cols=24 Identities=21% Similarity=0.220 Sum_probs=20.5
Q ss_pred CCcchHHHHHHHHhhcchhhhhhc
Q 045954 51 PMITSWEFHTVGRLVLPGELAKHT 74 (76)
Q Consensus 51 ~TitsrEIqtAvrLlLPGELaKhA 74 (76)
......+++.+..-++|.+++.|.
T Consensus 18 ~~~~~~~l~~~w~~ivg~~l~~~~ 41 (89)
T PF05258_consen 18 RALQLARLQQNWKQIVGPELAQHT 41 (89)
T ss_pred hhHHHHHHHHHHHHHhCHHHHccE
Confidence 556678899999999999999985
No 31
>PLN00160 histone H3; Provisional
Probab=53.07 E-value=24 Score=23.48 Aligned_cols=32 Identities=13% Similarity=0.159 Sum_probs=24.3
Q ss_pred HHHHHHHHHHH--HHhhcCCCCcchHHHHHHHHh
Q 045954 33 NIYIFKVLKQV--FARYKKKPMITSWEFHTVGRL 64 (76)
Q Consensus 33 ~~YiykVLKqV--La~~nkr~TitsrEIqtAvrL 64 (76)
..|+-.++... .+.+.+|-||.++|||-|.|+
T Consensus 58 EayLv~lfed~~lca~HakRVTl~~kD~~L~~ri 91 (97)
T PLN00160 58 EAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARRI 91 (97)
T ss_pred HHHHHHHHhhhHHHHHHhcccccchhhHHHHHHh
Confidence 34555555544 778999999999999999873
No 32
>PLN00161 histone H3; Provisional
Probab=51.91 E-value=27 Score=24.62 Aligned_cols=21 Identities=19% Similarity=0.180 Sum_probs=18.8
Q ss_pred HHhhcCCCCcchHHHHHHHHh
Q 045954 44 FARYKKKPMITSWEFHTVGRL 64 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvrL 64 (76)
.+.+.+|-||..+|||-|.||
T Consensus 105 caiHAkRVTlm~kDm~La~ri 125 (135)
T PLN00161 105 CAIHAKRVTIMPKDMQLARRI 125 (135)
T ss_pred HHHHhcCcccchhhHHHHHHh
Confidence 678899999999999999875
No 33
>PLN00157 histone H2A; Provisional
Probab=51.83 E-value=19 Score=25.25 Aligned_cols=34 Identities=26% Similarity=0.282 Sum_probs=27.9
Q ss_pred chhHHHHHHHHHHH----------HHhhcCCCCcchHHHHHHHH
Q 045954 30 KTYNIYIFKVLKQV----------FARYKKKPMITSWEFHTVGR 63 (76)
Q Consensus 30 esy~~YiykVLKqV----------La~~nkr~TitsrEIqtAvr 63 (76)
.+-.+|+--||.-+ -++.+++.-||+|.||.|++
T Consensus 47 ~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 47 AGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred CCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 34567888887766 56789999999999999997
No 34
>PLN00153 histone H2A; Provisional
Probab=51.68 E-value=23 Score=24.78 Aligned_cols=34 Identities=26% Similarity=0.258 Sum_probs=27.9
Q ss_pred chhHHHHHHHHHHH----------HHhhcCCCCcchHHHHHHHH
Q 045954 30 KTYNIYIFKVLKQV----------FARYKKKPMITSWEFHTVGR 63 (76)
Q Consensus 30 esy~~YiykVLKqV----------La~~nkr~TitsrEIqtAvr 63 (76)
.+-.+|+--||.-+ -++.|++.-||+|.||.||+
T Consensus 45 a~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 45 AGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 34567888877755 67889999999999999997
No 35
>PF14374 Ribos_L4_asso_C: 60S ribosomal protein L4 C-terminal domain; PDB: 3O5H_D 3IZS_D 3O58_D 3IZR_D 4A17_C 4A1C_C 4A1E_C 4A1A_C.
Probab=50.83 E-value=2.7 Score=27.11 Aligned_cols=12 Identities=42% Similarity=0.418 Sum_probs=10.5
Q ss_pred CcchHHHHHHHH
Q 045954 52 MITSWEFHTVGR 63 (76)
Q Consensus 52 TitsrEIqtAvr 63 (76)
-|.|.|||++||
T Consensus 18 iInSdEIQsvlr 29 (80)
T PF14374_consen 18 IINSDEIQSVLR 29 (80)
T ss_dssp HHHSHHHHCCCH
T ss_pred HhccHHHHHHHh
Confidence 478999999988
No 36
>PF00607 Gag_p24: gag gene protein p24 (core nucleocapsid protein); InterPro: IPR000721 The Gag protein from retroviruses, also known as p24, forms the inner protein layer of the nucleocapsid. This protein performs highly complex orchestrated tasks during the assembly, budding, maturation and infection stages of the viral replication cycle. During viral assembly, the proteins form membrane associations and self-associations that ultimately result in budding of an immature virion from the infected cell. Gag precursors also function during viral assembly to selectively bind and package two plus strands of genomic RNA. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.; GO: 0016032 viral reproduction; PDB: 1BMX_A 1SJH_C 1SJE_C 1U57_A 1FGL_B 1G03_A 2XT1_A 2JO0_A 2L6E_A 2HJL_C ....
Probab=50.79 E-value=25 Score=25.38 Aligned_cols=20 Identities=5% Similarity=0.205 Sum_probs=16.2
Q ss_pred ccccCcchhHHHHHHHHHHH
Q 045954 24 CAKKSIKTYNIYIFKVLKQV 43 (76)
Q Consensus 24 rkkkr~esy~~YiykVLKqV 43 (76)
-+...+|+|..||-|+++.+
T Consensus 128 I~QGp~Epf~dFv~rl~~a~ 147 (206)
T PF00607_consen 128 IKQGPKEPFADFVDRLQKAI 147 (206)
T ss_dssp H-S-TTSHHHHHHHHHHHHH
T ss_pred hhhccccchHHHHHHHHHHH
Confidence 34556899999999999999
No 37
>PF14513 DAG_kinase_N: Diacylglycerol kinase N-terminus; PDB: 1TUZ_A.
Probab=49.91 E-value=20 Score=25.00 Aligned_cols=44 Identities=32% Similarity=0.482 Sum_probs=30.0
Q ss_pred chhHHHHHHHHHHH---------HHhhcCCCCcchHHHHHHHHhh----cchhhhhh
Q 045954 30 KTYNIYIFKVLKQV---------FARYKKKPMITSWEFHTVGRLV----LPGELAKH 73 (76)
Q Consensus 30 esy~~YiykVLKqV---------La~~nkr~TitsrEIqtAvrLl----LPGELaKh 73 (76)
.-|..|=-|=||.| |++||...+|.-.-++.=++.. ||.+|.+|
T Consensus 17 q~y~eys~kklkdvl~eF~~~g~~~~~~~~~~Id~egF~~Fm~~yLe~d~P~~lc~h 73 (138)
T PF14513_consen 17 QKYSEYSTKKLKDVLKEFHGDGSLAKYNPEEPIDYEGFKLFMKTYLEVDLPEDLCQH 73 (138)
T ss_dssp HHHHHH----HHHHHHHH-HTSGGGGGEETTEE-HHHHHHHHHHHTT-S--HHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhcCCcccccCCCCCcCHHHHHHHHHHHHcCCCCHHHHHH
Confidence 35788888888888 8899999999988877766665 68888887
No 38
>PLN00156 histone H2AX; Provisional
Probab=48.75 E-value=28 Score=24.68 Aligned_cols=33 Identities=27% Similarity=0.276 Sum_probs=26.6
Q ss_pred hhHHHHHHHHHHH----------HHhhcCCCCcchHHHHHHHH
Q 045954 31 TYNIYIFKVLKQV----------FARYKKKPMITSWEFHTVGR 63 (76)
Q Consensus 31 sy~~YiykVLKqV----------La~~nkr~TitsrEIqtAvr 63 (76)
+-.+|+--||.-+ -++.+++.-||+|.||.||+
T Consensus 51 ~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 51 GAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 4567777777655 56789999999999999997
No 39
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=46.63 E-value=66 Score=19.55 Aligned_cols=33 Identities=9% Similarity=0.014 Sum_probs=25.5
Q ss_pred hHHHHHHHHHHH--HHhhcCCCCcchHHHHHHHHh
Q 045954 32 YNIYIFKVLKQV--FARYKKKPMITSWEFHTVGRL 64 (76)
Q Consensus 32 y~~YiykVLKqV--La~~nkr~TitsrEIqtAvrL 64 (76)
+..|+-.+.+.. ++....|.+.+..||.-|+.-
T Consensus 36 ~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~ 70 (77)
T smart00576 36 LQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN 70 (77)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 456666666666 777889999999999988753
No 40
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=46.40 E-value=25 Score=22.15 Aligned_cols=31 Identities=19% Similarity=0.359 Sum_probs=20.0
Q ss_pred HHHHHHHHHHH------HHhhcCCCCcchHHHHHHHH
Q 045954 33 NIYIFKVLKQV------FARYKKKPMITSWEFHTVGR 63 (76)
Q Consensus 33 ~~YiykVLKqV------La~~nkr~TitsrEIqtAvr 63 (76)
..-+|+-+..+ ++++-+|+||+..|+.=.+|
T Consensus 35 ~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 35 TELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 34455555544 88999999999999764443
No 41
>TIGR02442 Cob-chelat-sub cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.
Probab=44.84 E-value=38 Score=28.18 Aligned_cols=27 Identities=22% Similarity=0.320 Sum_probs=24.6
Q ss_pred HHhhcCCCCcchHHHHHHHHhhcchhh
Q 045954 44 FARYKKKPMITSWEFHTVGRLVLPGEL 70 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvrLlLPGEL 70 (76)
+|-.+.+.+++..||+.|++|+|+.-+
T Consensus 283 ~AaL~gr~~V~~~Dv~~A~~lvL~hR~ 309 (633)
T TIGR02442 283 LAALDGRRRVTAEDVREAAELVLPHRR 309 (633)
T ss_pred HHHHcCCCcCCHHHHHHHHHHHhhhhc
Confidence 888999999999999999999997654
No 42
>PF03477 ATP-cone: ATP cone domain; InterPro: IPR005144 The ATP-cone is an evolutionarily mobile, ATP-binding regulatory domain which is found in a variety of proteins including ribonucleotide reductases, phosphoglycerate kinases and transcriptional regulators []. In ribonucleotide reductase protein R1 (P28903 from SWISSPROT) from Escherichia coli this domain is located at the N terminus, and is composed mostly of helices []. It forms part of the allosteric effector region and contains the general allosteric activity site in a cleft located at the tip of the N-terminal region []. This site binds either ATP (activating) or dATP (inhibitory), with the base bound in a hydrophobic pocket and the phosphates bound to basic residues. Substrate binding to this site is thought to affect enzyme activity by altering the relative positions of the two subunits of ribonucleotide reductase.; PDB: 2XO4_A 1RLR_A 7R1R_B 5R1R_A 2XO5_B 2XAW_A 2R1R_C 2XAY_B 2X0X_C 2XAZ_A ....
Probab=42.42 E-value=33 Score=20.70 Aligned_cols=33 Identities=15% Similarity=0.058 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHhhcC--CCCcchHHHHHHHHhhc
Q 045954 34 IYIFKVLKQVFARYKK--KPMITSWEFHTVGRLVL 66 (76)
Q Consensus 34 ~YiykVLKqVLa~~nk--r~TitsrEIqtAvrLlL 66 (76)
.....+..+|+..... ...||..|||..|.-.|
T Consensus 35 ~~~~~i~~~V~~~l~~~~~~~is~~eI~~~v~~~L 69 (90)
T PF03477_consen 35 EDAEEIASEVENKLYDSGKEEISTEEIQDIVENAL 69 (90)
T ss_dssp T-HHHHHHHHHTC-ST----TEEHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhccCCCeeHHHHHHHHHHHH
Confidence 3466777777555544 34899999999997665
No 43
>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.
Probab=37.53 E-value=59 Score=26.94 Aligned_cols=27 Identities=19% Similarity=0.143 Sum_probs=24.3
Q ss_pred HHhhcCCCCcchHHHHHHHHhhcchhh
Q 045954 44 FARYKKKPMITSWEFHTVGRLVLPGEL 70 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvrLlLPGEL 70 (76)
+|-.+.|.+++..||+.|++|+|+.-+
T Consensus 237 ~Aal~gr~~V~~~Dv~~a~~lvl~hR~ 263 (589)
T TIGR02031 237 HAALHGRTEVTEEDLKLAVELVLLPRA 263 (589)
T ss_pred HHHHhCCCCCCHHHHHHHHHHHhhhhc
Confidence 888999999999999999999997543
No 44
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=35.88 E-value=65 Score=25.34 Aligned_cols=27 Identities=22% Similarity=0.308 Sum_probs=24.5
Q ss_pred HHhhcCCCCcchHHHHHHHHhhcchhh
Q 045954 44 FARYKKKPMITSWEFHTVGRLVLPGEL 70 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvrLlLPGEL 70 (76)
+|-.+.|..++..||+.++.++|+.-+
T Consensus 301 ~Aal~GR~~V~pdDv~~~a~~vL~HR~ 327 (350)
T CHL00081 301 LAAFEGRTEVTPKDIFKVITLCLRHRL 327 (350)
T ss_pred HHHHcCCCCCCHHHHHHHHHHHHHHhC
Confidence 888999999999999999999997644
No 45
>KOG3090 consensus Prohibitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=35.43 E-value=25 Score=27.63 Aligned_cols=36 Identities=28% Similarity=0.305 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHhhcCCCCcchHHHHHHHHhhcchhhhh
Q 045954 34 IYIFKVLKQVFARYKKKPMITSWEFHTVGRLVLPGELAK 72 (76)
Q Consensus 34 ~YiykVLKqVLa~~nkr~TitsrEIqtAvrLlLPGELaK 72 (76)
+-|+.|||.|.++||-..-||-|| +|-+++--+|-.
T Consensus 132 SIinEvLKaVVAqfNASqLITQRe---~VSrliRk~L~e 167 (290)
T KOG3090|consen 132 SIINEVLKAVVAQFNASQLITQRE---QVSRLIRKILTE 167 (290)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHH---HHHHHHHHHHHH
Confidence 457889999999999999999987 344444444433
No 46
>COG2361 Uncharacterized conserved protein [Function unknown]
Probab=33.37 E-value=1e+02 Score=21.30 Aligned_cols=45 Identities=20% Similarity=0.297 Sum_probs=34.3
Q ss_pred cchhHHHHHHHHHHH--HHhhcCCCCc----chHHHHHHH--Hhhcchhhhhh
Q 045954 29 IKTYNIYIFKVLKQV--FARYKKKPMI----TSWEFHTVG--RLVLPGELAKH 73 (76)
Q Consensus 29 ~esy~~YiykVLKqV--La~~nkr~Ti----tsrEIqtAv--rLlLPGELaKh 73 (76)
+..++.|++.+|..+ +..|.+--|. .+.++|.|| .|.+=||-+||
T Consensus 3 ~k~~~~yL~diL~a~~~i~~yT~~~d~~~F~~~~~~~dAvir~L~iIGEa~k~ 55 (117)
T COG2361 3 KKDDRVYLYDILQAAERIEEYTKDMDYEEFIADKLTQDAVIRNLEIIGEATKR 55 (117)
T ss_pred cccHHHHHHHHHHHHHHHHHHhccCCHHHHHHhHHHHHHHHHHHHHHHHHHhh
Confidence 456789999999987 6777776664 678888887 46677887776
No 47
>PTZ00252 histone H2A; Provisional
Probab=32.97 E-value=63 Score=22.82 Aligned_cols=34 Identities=24% Similarity=0.270 Sum_probs=26.4
Q ss_pred chhHHHHHHHHHHH------H----H--hhcCCCCcchHHHHHHHH
Q 045954 30 KTYNIYIFKVLKQV------F----A--RYKKKPMITSWEFHTVGR 63 (76)
Q Consensus 30 esy~~YiykVLKqV------L----a--~~nkr~TitsrEIqtAvr 63 (76)
.+-.+|+--||.-+ | + +.|++.-|++|.||.||+
T Consensus 46 a~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 46 ASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred CccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 44578888888765 2 2 347889999999999997
No 48
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.
Probab=32.54 E-value=44 Score=25.95 Aligned_cols=27 Identities=22% Similarity=0.315 Sum_probs=24.2
Q ss_pred HHhhcCCCCcchHHHHHHHHhhcchhh
Q 045954 44 FARYKKKPMITSWEFHTVGRLVLPGEL 70 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvrLlLPGEL 70 (76)
+|-.+.|..++..||+.+++++|+.-+
T Consensus 288 ~Aal~GR~~V~~dDv~~~a~~vL~HR~ 314 (337)
T TIGR02030 288 LAAFEGRTEVTVDDIRRVAVLALRHRL 314 (337)
T ss_pred HHHHcCCCCCCHHHHHHHHHHHHHHhC
Confidence 788899999999999999999987543
No 49
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.92 E-value=20 Score=31.66 Aligned_cols=43 Identities=14% Similarity=0.206 Sum_probs=36.1
Q ss_pred cccCcchhHHHHHHHHHHH--------------------HHhhcCCCCc-chHHHHHHHHhhcc
Q 045954 25 AKKSIKTYNIYIFKVLKQV--------------------FARYKKKPMI-TSWEFHTVGRLVLP 67 (76)
Q Consensus 25 kkkr~esy~~YiykVLKqV--------------------La~~nkr~Ti-tsrEIqtAvrLlLP 67 (76)
.|+-.|||+.|+...|.|. -..-|-|+|+ |.-||..-.|||+.
T Consensus 48 qRry~es~s~y~rq~l~~~~~P~vd~i~gl~paiai~Q~~~~~n~RSTVgT~Tei~~~LrlLfa 111 (924)
T TIGR00630 48 QRRYVESLSAYARQFLGVMDKPDVDSIEGLSPAISIDQKTTSHNPRSTVGTITEIYDYLRLLFA 111 (924)
T ss_pred HHHHHhhccHHHHHhhccCCCCCcCeEcCCCceEEEeccCCCCCCCcccchHHHHHHHHHHHHH
Confidence 4556899999999999988 3356889999 99999999999853
No 50
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=29.96 E-value=99 Score=21.89 Aligned_cols=20 Identities=35% Similarity=0.260 Sum_probs=18.4
Q ss_pred HHhhcCCCCcchHHHHHHHH
Q 045954 44 FARYKKKPMITSWEFHTVGR 63 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvr 63 (76)
-++-|+++-|++|.||-|++
T Consensus 72 aardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 72 AARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred HhhhcCccccChHHHHHHHh
Confidence 66789999999999999998
No 51
>PF09193 CholecysA-Rec_N: Cholecystokinin A receptor, N-terminal; InterPro: IPR015276 This entry represents the extracellular N-terminal domain of the cholecystokinin A receptor. This domain adopts a tertiary structure consisting of a few helical turns and a disulphide-cross linked loop. It is required for interaction of the cholecystokinin A receptor with its corresponding hormonal ligand []. ; PDB: 1D6G_A.
Probab=28.94 E-value=19 Score=21.42 Aligned_cols=13 Identities=23% Similarity=0.366 Sum_probs=9.2
Q ss_pred chHHHHHHHHhhc
Q 045954 54 TSWEFHTVGRLVL 66 (76)
Q Consensus 54 tsrEIqtAvrLlL 66 (76)
.|+|.|-||+++|
T Consensus 35 pske~qpaVqILL 47 (47)
T PF09193_consen 35 PSKEWQPAVQILL 47 (47)
T ss_dssp S-SSHHHHHHS--
T ss_pred ChhHHhhhHhhhC
Confidence 7889999999886
No 52
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=28.93 E-value=23 Score=31.43 Aligned_cols=43 Identities=16% Similarity=0.229 Sum_probs=36.2
Q ss_pred cccCcchhHHHHHHHHHHH--------------------HHhhcCCCCc-chHHHHHHHHhhcc
Q 045954 25 AKKSIKTYNIYIFKVLKQV--------------------FARYKKKPMI-TSWEFHTVGRLVLP 67 (76)
Q Consensus 25 kkkr~esy~~YiykVLKqV--------------------La~~nkr~Ti-tsrEIqtAvrLlLP 67 (76)
.|+-.|||+.|+...|.|. -..-|-|+|+ |.-||..-.|||+.
T Consensus 52 qRry~Es~s~y~rq~l~~~~~P~vd~i~gl~p~Iai~Q~~~~~n~RSTVgT~Tei~~~LrlLfa 115 (943)
T PRK00349 52 QRRYVESLSAYARQFLGQMDKPDVDSIEGLSPAISIDQKTTSHNPRSTVGTVTEIYDYLRLLYA 115 (943)
T ss_pred HHHHHhhccHHHHHhhccCCCCCcCeEcCCCceEEEEecCCCCCCCccchhHHHHHHHHHHHHH
Confidence 4556799999999999988 3356899999 89999999999853
No 53
>KOG3083 consensus Prohibitin [Posttranslational modification, protein turnover, chaperones]
Probab=28.79 E-value=54 Score=25.63 Aligned_cols=25 Identities=32% Similarity=0.464 Sum_probs=22.8
Q ss_pred HHHHHHHHHhhcCCCCcchHHHHHH
Q 045954 37 FKVLKQVFARYKKKPMITSWEFHTV 61 (76)
Q Consensus 37 ykVLKqVLa~~nkr~TitsrEIqtA 61 (76)
..|||+|.++++--.-||-||+-++
T Consensus 124 ~eiLKsVVa~FdA~eliTqRe~vS~ 148 (271)
T KOG3083|consen 124 TEILKSVVARFDAGELITQRELVSR 148 (271)
T ss_pred HHHHHHHHHhccccchhhhhHHHHH
Confidence 5899999999999999999998776
No 54
>PF14164 YqzH: YqzH-like protein
Probab=26.84 E-value=1.6e+02 Score=18.35 Aligned_cols=31 Identities=13% Similarity=0.174 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHhhc---CCCCcchHHHHHHHHh
Q 045954 34 IYIFKVLKQVFARYK---KKPMITSWEFHTVGRL 64 (76)
Q Consensus 34 ~YiykVLKqVLa~~n---kr~TitsrEIqtAvrL 64 (76)
.+|.|.+.++|-+|+ ....||++|.+.=++-
T Consensus 4 k~I~Kmi~~~l~QYg~d~~~~pls~~E~~~L~~~ 37 (64)
T PF14164_consen 4 KLIEKMIINCLRQYGYDVECMPLSDEEWEELCKH 37 (64)
T ss_pred HHHHHHHHHHHHHhCCcccCCCCCHHHHHHHHHH
Confidence 478999999999994 5678899987664443
No 55
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=25.87 E-value=1e+02 Score=21.84 Aligned_cols=31 Identities=29% Similarity=0.329 Sum_probs=24.4
Q ss_pred HHHHHHHHHHH----------HHhhcCCCCcchHHHHHHHH
Q 045954 33 NIYIFKVLKQV----------FARYKKKPMITSWEFHTVGR 63 (76)
Q Consensus 33 ~~YiykVLKqV----------La~~nkr~TitsrEIqtAvr 63 (76)
.+|+--||.-. -++-++..-|++|.||-|+|
T Consensus 50 ~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 50 PVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 45666666544 67889999999999999987
No 56
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=25.65 E-value=1.1e+02 Score=25.57 Aligned_cols=27 Identities=19% Similarity=0.202 Sum_probs=24.3
Q ss_pred HHhhcCCCCcchHHHHHHHHhhcchhh
Q 045954 44 FARYKKKPMITSWEFHTVGRLVLPGEL 70 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvrLlLPGEL 70 (76)
+|-.+.+..++..+|+.|+.|+|+.-+
T Consensus 229 ~AaL~Gr~~V~~~dv~~Aa~lvL~hR~ 255 (584)
T PRK13406 229 AAALAGRTAVEEEDLALAARLVLAPRA 255 (584)
T ss_pred HHHHcCCCCCCHHHHHHHHHHHHHhhc
Confidence 888899999999999999999997543
No 57
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=25.49 E-value=76 Score=27.29 Aligned_cols=22 Identities=18% Similarity=0.113 Sum_probs=20.3
Q ss_pred HHhhcCCCCcchHHHHHHHHhh
Q 045954 44 FARYKKKPMITSWEFHTVGRLV 65 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvrLl 65 (76)
+.+..+|.++|..||..|.|.+
T Consensus 55 fm~hskR~kLtv~DV~~ALr~~ 76 (576)
T KOG2549|consen 55 FMVHSKRTKLTVDDVDYALRSL 76 (576)
T ss_pred HhhcCCCCcCcHHHHHHHHhhc
Confidence 8899999999999999999864
No 58
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=25.34 E-value=47 Score=25.78 Aligned_cols=26 Identities=15% Similarity=0.279 Sum_probs=20.6
Q ss_pred HHhhcCCCCcchHHHHHHHH----hhcchh
Q 045954 44 FARYKKKPMITSWEFHTVGR----LVLPGE 69 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvr----LlLPGE 69 (76)
||.+.+..||-.+|||-.+. +-|||.
T Consensus 199 LAKHRKsdtlEvrDIqLhLEr~~Nm~iPgf 228 (258)
T KOG1142|consen 199 LAKHRKSDTVEVRDIQLHLERNFNMEIPGF 228 (258)
T ss_pred HHHhcccCccchhheeeeeeccccccCCCc
Confidence 99999999999999986543 335654
No 59
>PF12412 DUF3667: Protein of unknown function (DUF3667); InterPro: IPR022134 This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. There is a single completely conserved residue P that may be functionally important.
Probab=23.88 E-value=61 Score=18.41 Aligned_cols=16 Identities=44% Similarity=0.910 Sum_probs=12.2
Q ss_pred HHHHHHhhc-chhhhhh
Q 045954 58 FHTVGRLVL-PGELAKH 73 (76)
Q Consensus 58 IqtAvrLlL-PGELaKh 73 (76)
..|...|++ ||++.+.
T Consensus 5 ~rTl~~L~~rPG~~~~~ 21 (46)
T PF12412_consen 5 FRTLRDLLLRPGEVTRE 21 (46)
T ss_pred HHHHHHHHhCHHHHHHH
Confidence 467777888 9998864
No 60
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=23.87 E-value=21 Score=25.26 Aligned_cols=22 Identities=18% Similarity=0.132 Sum_probs=19.2
Q ss_pred HHhhcCCCCcchHHHHHHHHhh
Q 045954 44 FARYKKKPMITSWEFHTVGRLV 65 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvrLl 65 (76)
.+.+.+|-||-+.|||-|.++.
T Consensus 112 cAihAkRVTimpkdiQlArrir 133 (137)
T KOG1745|consen 112 CAIHAKRVTIMPKDIQLARRIR 133 (137)
T ss_pred hhhccceeEecccceehhhhcc
Confidence 5678999999999999999943
No 61
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=23.20 E-value=31 Score=23.41 Aligned_cols=40 Identities=23% Similarity=0.325 Sum_probs=28.1
Q ss_pred HHHHHHHHHHH------HHhhcCCC-CcchHHHHHHHHhhcchhhhh
Q 045954 33 NIYIFKVLKQV------FARYKKKP-MITSWEFHTVGRLVLPGELAK 72 (76)
Q Consensus 33 ~~YiykVLKqV------La~~nkr~-TitsrEIqtAvrLlLPGELaK 72 (76)
++|++||+..= +-+|.+.- -++.+|+|.-..-+-|-|+.+
T Consensus 51 ~sYlfRV~t~~MTy~~Q~k~Ye~a~~~~~~~~lqkRle~l~~eE~~~ 97 (104)
T PF11460_consen 51 SSYLFRVVTGKMTYMQQRKDYEEAVDQLTNEELQKRLEELSPEELEA 97 (104)
T ss_pred hHHHhhhccCCCcHHHHHHHHHHHHHHHhHHHHHHHHHhCCHHHHHH
Confidence 57888887533 55554332 567778888888888888765
No 62
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=23.12 E-value=99 Score=22.74 Aligned_cols=22 Identities=9% Similarity=-0.017 Sum_probs=19.2
Q ss_pred HHhhcCCCCcchHHHHHHHHhh
Q 045954 44 FARYKKKPMITSWEFHTVGRLV 65 (76)
Q Consensus 44 La~~nkr~TitsrEIqtAvrLl 65 (76)
-|+-.+|.||+-.||-.|+--|
T Consensus 78 kC~~EkRKTIngdDllwAm~tL 99 (168)
T KOG0869|consen 78 KCQREKRKTINGDDLLWAMSTL 99 (168)
T ss_pred HHHHHhcCcccHHHHHHHHHHc
Confidence 7888999999999999998643
No 63
>PF04406 TP6A_N: Type IIB DNA topoisomerase; InterPro: IPR013049 This entry represents the N-terminal domain found in Spo11, a meiotic recombination protein found in eukaryotes, and in subunit A of topoisomerase VI, a type IIB topoisomerase found predominantly in archaea [, ]. These two types of proteins share structural homology. Spo11 is a meiosis-specific protein that is responsible for the initiation of recombination through the formation of DNA double-strand breaks by a type II DNA topoisomerase-like activity. Spo11 acts in conjunction with several other proteins, including Rec102 in yeast, to bring about meiotic recombination []. DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. They can be divided into two classes: type I enzymes (5.99.1.2 from EC, topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC, topoisomerases II, IV and VI) break double-strand DNA []. Topoisomerase VI is a type IIB enzymes that assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis. The B subunit is structurally similar to the ATPase domain of type IIA topoisomerases, but the A subunit is distinct, and instead shares homology with the Spo11 protein. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003824 catalytic activity, 0005524 ATP binding, 0006259 DNA metabolic process, 0005694 chromosome; PDB: 1D3Y_B 2ZBK_A 2Q2E_A.
Probab=22.84 E-value=88 Score=18.53 Aligned_cols=25 Identities=12% Similarity=0.211 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHhhcCCCCcchHHH
Q 045954 34 IYIFKVLKQVFARYKKKPMITSWEF 58 (76)
Q Consensus 34 ~YiykVLKqVLa~~nkr~TitsrEI 58 (76)
.-+.+||..+........+.|-|||
T Consensus 9 a~~l~vl~~i~~~l~~~~~~T~Rdi 33 (68)
T PF04406_consen 9 AQLLRVLAIIHELLQNNKTSTKRDI 33 (68)
T ss_dssp HHHHHHHHHHHHHHHTT--EEHHHH
T ss_pred HHHHHHHHHHHHHHHcCCccchHHH
Confidence 3466788888666666677788886
No 64
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=21.93 E-value=2e+02 Score=21.27 Aligned_cols=33 Identities=15% Similarity=0.245 Sum_probs=24.3
Q ss_pred hHHHHHHHHHHHHHhhcCCCCcchHHHHHHHHhh
Q 045954 32 YNIYIFKVLKQVFARYKKKPMITSWEFHTVGRLV 65 (76)
Q Consensus 32 y~~YiykVLKqVLa~~nkr~TitsrEIqtAvrLl 65 (76)
|-+|+--+-.+ +|+-++|.||+..||-.|++-+
T Consensus 46 Fv~~Lts~s~e-~A~~q~rKt~sadDVl~aL~Ei 78 (172)
T KOG0870|consen 46 FVIFLTSVSNE-IAKDQKRKTISADDVLKALDEI 78 (172)
T ss_pred HHHHHHHHHHH-HHHhcccCcccHHHHHHHHHHh
Confidence 34444333333 8999999999999999998754
No 65
>PHA02937 hypothetical protein; Provisional
Probab=21.87 E-value=74 Score=25.24 Aligned_cols=15 Identities=47% Similarity=0.673 Sum_probs=12.1
Q ss_pred cchhHHHHHHHHHHH
Q 045954 29 IKTYNIYIFKVLKQV 43 (76)
Q Consensus 29 ~esy~~YiykVLKqV 43 (76)
-|.--+|+|++++||
T Consensus 16 IekQyik~ykL~kQv 30 (310)
T PHA02937 16 IEKQYIKLYKLLKQV 30 (310)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344568999999999
No 66
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=20.54 E-value=1.4e+02 Score=20.98 Aligned_cols=16 Identities=19% Similarity=-0.035 Sum_probs=13.3
Q ss_pred CCcchHHHHHHHHhhc
Q 045954 51 PMITSWEFHTVGRLVL 66 (76)
Q Consensus 51 ~TitsrEIqtAvrLlL 66 (76)
..++..|||..|.-.|
T Consensus 101 ~~IsveEIqDiVE~~L 116 (154)
T PRK00464 101 REVPSKEIGELVMEEL 116 (154)
T ss_pred CCCCHHHHHHHHHHHH
Confidence 5799999999997544
Done!